Thermodynamics of hybridization in DNA microarrays: Theory and Applications

DNA microarrays have been intensively used in the past years for gene expression studies and for the analysis of full genomes. These devices are high throughput and rely on the hybridization between target sequences in solution and sequences covalently linked at a solid surface. During this talk I will review some results of the analysis of dedicated experiments to characterize the thermodynamics of the hybridization process in microarrays. I will show that accurate nearest-neighbor model parameters can be obtained from the analysis of hybridizations with sequences carrying one or more mismatches. These inputs can be used to design accurate diagnostic tools for the analysis of samples containing mutations. As an example the case of HIV will be discussed.

References:

J. Hooyberghs, M. Baiesi, A. Ferrantini and E. Carlon "Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays" Phys. Rev. E 81, 012901 (2010)

W. Hadiwikarta, J.-C.Walter, J. Hooyberghs and E. Carlon , "Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond" Nucl. Acids Res. 40, e138 (2012)

W. Hadiwikarta, B. Van Dorst, K. Hollanders, L. Stuyver, E. Carlon and J. Hooyberghs, "Targeted resequencing of HIV variants by microarray thermodynamics" Nucl. Acids Res. 41, e173 (2013)